Kunkel's first marriage was to singer Leah Kunkel, younger sister of Cass Elliot, and together they raised Elliot's daughter, Owen Vanessa as well as having their own son Nathaniel, now an Emmy Award-winning sound engineer.

Kunkel's second marriage was to singer Nicolette Larson (best known for her hit single the Neil Young-penned Lotta Love) in 1990 and they had a daughter Elsie-May Larson-Kunkel. Larson died of cerebral edema on December the 16th, 1997 at the age of 45.